Related papers: Hierarchical Framework for Predicting Entropies in…
In many areas of science and engineering, computer simulations are widely used as proxies for physical experiments, which can be infeasible or unethical. Such simulations can often be computationally expensive, and an emulator can be…
The data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
Aggregation transitions in disordered mesoscopic systems play an important role in several areas of knowledge, from materials science to biology. The lack of a thermodynamic limit in systems that are intrinsically finite makes the…
Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
A numerical model is built, simulating the principles of kinetic gas theory, to predict pressures of molecules in a spherical pressure vessel; the model tracks a single particle and multiplies the force on the spherical walls by a mole of…
Hierarchical categorical variables often exhibit many levels (high granularity) and many classes within each level (high dimensionality). This may cause overfitting and estimation issues when including such covariates in a predictive model.…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics like work, heat and entropy production to the level of individual trajectories of well-defined…
We introduce a generalized machine learning framework to probabilistically parameterize upper-scale models in the form of nonlinear PDEs consistent with a continuum theory, based on coarse-grained atomistic simulation data of mechanical…
Computational models of complex physical systems often rely on simplifying assumptions which inevitably introduce model error, with consequent predictive errors. Given data on model observables, the estimation of parameterized model-error…
We present a hierarchical Bayesian inference approach to estimating the structural properties and the phase space center of a globular cluster (GC) given the spatial and kinematic information of its stars based on lowered isothermal cluster…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
Bottom-up coarse-grained molecular dynamics models are parameterized using complex effective Hamiltonians. These models are typically optimized to approximate high dimensional data from atomistic simulations. In contrast, human validation…
The primary objective of this work is to develop coarse-graining schemes for stochastic many-body microscopic models and quantify their effectiveness in terms of a priori and a posteriori error analysis. In this paper we focus on stochastic…
The general framework of entropic dynamics is used to formulate a relational quantum dynamics. The main new idea is to use tools of information geometry to develop an entropic measure of the mismatch between successive configurations of a…
The recursive property of entropy is well known in information theory; however, the concept is underutilized in thermodynamics, despite being the field where the concept of entropy originated. The zentropy approach is built on this idea,…
A general scheme, which includes constructions of coarse-grained (CG) models, weighted ensemble dynamics (WED) simulations and cluster analyses (CA) of stable states, is presented to detect dynamical and thermodynamical properties in…
As has been shown elsewhere, a reasonable model of the loss of entanglement or correlation that occurs in quantum computations is one which assumes that they can effectively be predicted by a framework that presupposes the presence of…
The automated construction of coarse-grained models represents a pivotal component in computer simulation of physical systems and is a key enabler in various analysis and design tasks related to uncertainty quantification. Pertinent methods…